resultsupload.R

library(here)
library(data.table)
library(glue)
library(googlesheets4)


## NOTE new sheet
## create an ID to access the googlesheets results sheet
yourl <- "https://docs.google.com/spreadsheets/d/1yRUIErcA9H_1rbgG46WoKARt9-8t94tnJRS3X91gzFo/edit#gid=0"
shid <- as.character(as_sheets_id(yourl))


## utility function
upload.to.sheets <- function(basename,filename,sheetid
                             ){
  filename <- gsub("\\.csv$","",filename) #safety in case csv included at and
  fn <- glue(basename) + filename + ".csv"
  tmp <- fread(file=fn)
  write_sheet(tmp,sheetid,sheet=filename)
}

## upload relevant table data
upload.to.sheets(here('model/outdata/'),'cascadetab',shid) #first will need to re-authenticate

## rest can be run as block
flz1 <- c(
 "ACFcascade.1.csv",   "ACFcascadecdr.1.csv","ACFcascadehi.1.csv",
 "ACFcascadelo.1.csv", "ACFcascadetxd.1.csv","cascadetab.csv",
 "CEAC50.csv",         "CEAC50cdr.csv",      "CEAC50hi.csv",
 "CEAC50lo.csv",       "CEAC50pt.1.csv",     "CEAC50ptcdr.1.csv",
 "CEAC50pthi.1.csv",   "CEAC50ptlo.1.csv",   "CEAC50pttxd.1.csv",
 "CEAC50txd.csv",      "CEAC50all.1.csv",     "CEAC50allcdr.1.csv",
 "CEAC50allhi.1.csv",   "CEAC50alllo.1.csv",   "CEAC50alltxd.1.csv",
 "ICERagept.1.csv",    "ICERageptcdr.1.csv",
 "ICERagepthi.1.csv",  "ICERageptlo.1.csv",  "ICERagepttxd.1.csv",
 "ICERall.1.csv",      "ICERallcdr.1.csv",   "ICERallhi.1.csv",
 "ICERalllo.1.csv",    "ICERalltxd.1.csv")
for( fn in flz1)
  upload.to.sheets(here('model/outdata//'),fn,shid)

Sys.sleep(120) #wait a bit so as not to annoy google

flz2 <- c("ICERatt.csv",
 "ICERattcdr.csv",     "ICERatthi.csv",      "ICERattlo.csv",
 "ICERatttxd.csv",     "ICERpt.1.csv",       "ICERptcdr.1.csv",
 "ICERpthi.1.csv",     "ICERptlo.1.csv",     "ICERpttxd.1.csv",
 "ICERSatt.csv",       "ICERSattcdr.csv",    "ICERSatthi.csv",
 "ICERSattlo.csv",     "ICERSatttxd.csv",    "PTC.csv",
 "ptsuccess.csv",      "txsuccess.csv"
)
for( fn in flz2)
  upload.to.sheets(here('model/outdata//'),fn,shid)


## need article tables
yurl <- "https://docs.google.com/spreadsheets/d/1p8ZT0BP-lABM0W0z6V6I_4cg51ndPYyyUKn11Cq9f5M/edit#gid=0"
shidneat <- as.character(as_sheets_id(yurl))

## ---- Table 1 -------
## build 1st
load(here('model/data/Table1ATT.Rdata'))
load(here('model/data/Table1PT.Rdata'))
load(here('model/data/Table1PTcost.Rdata'))

## ensure correct naming
names(Table1ATT) <- gsub("ote","ôte",names(Table1ATT))
names(Table1PT) <- gsub("ote","ôte",names(Table1PT))
names(Table1PTcost) <- gsub("ote","ôte",names(Table1PTcost))

setcolorder(Table1PTcost,names(Table1PT))

Table1 <- rbindlist(list(Table1ATT,Table1PT,Table1PTcost))

write_sheet(Table1,shidneat,sheet="Tab1RAW")

## ---- Table 2 -------

## ATT part
load(here('model/outdata/Table2ATT.Rdata'))
write_sheet(Table2ATT,shidneat,sheet="Tab2ATT")

## PT part
load(here('model/outdata/Table2PT.1.Rdata'))
write_sheet(Table2PT,shidneat,sheet="Tab2PT")

## combined intervention
load(here('model/outdata/Table2both.1.Rdata'))
write_sheet(Table2both,shidneat,sheet="Tab2combined")

## backgrounds stats for results
upload.to.sheets(here('dataprep/outdata/'),"Pstats.csv",shidneat)
upload.to.sheets(here('dataprep/outdata/'),"Dstats.csv",shidneat)
upload.to.sheets(here('dataprep/outdata/'),"Tstats.csv",shidneat)

## --- SA table ---
sa.base <- fread(here('model/outdata/ICERall.1.csv'))
sa.dalys <- fread(here('model/outdata/ICERalldalys.1.csv'))
sa.hi <- fread(here('model/outdata/ICERallhi.1.csv'))
sa.lo <- fread(here('model/outdata/ICERalllo.1.csv'))
sa.succ <- fread(here('model/outdata/ICERalltxd.1.csv'))


names(sa.base)[3] <- 'Base case'
names(sa.dalys)[3] <- 'Life years'
names(sa.hi)[3] <- '5% discount rate'
names(sa.lo)[3] <- '0% discount rate'
names(sa.succ)[3] <- 'ATT/TPT completion improvement included'

SAll <- Reduce(merge,list(sa.base,sa.dalys,sa.hi,sa.lo,sa.succ))

write_sheet(SAll,shidneat,sheet="SAll")